qPCR.rna.mean.reps: qPCR RNA expression experimental replicates mean calculator.

In sebastian-gregoricchio/Rseb: An R-package for NGS data managing and visualization

qPCR RNA expression experimental replicates mean calculator.

Description

This function allows to generate a table and a plot result (FoldChange and normalized Expression) of the mean of different replicates of an experiment starting from analyses performed by qPCR.rna.exp.

Usage

qPCR.rna.mean.reps(
  reps.list,
  reference.sample = NULL,
  exclude.samples = NULL,
  exclude.housekeeping.genes = TRUE,
  plot.color = "#d1718b",
  fix.y.axis = FALSE,
  text.size = 3,
  x.labels.rotation = 45
)

Arguments

reps.list	A list of qPCR.rna.exp result objects.
reference.sample	Single string indicating the name of the sample to use as reference for the computation of the FoldChanges. By default NULL: if the input is a list of qPCR.rna.exp objects, the reference.sample is retrieved automatically. However, if the number of reference used are multiple and/or not shared among replicates, the first sample in the order is used as reference.
exclude.samples	String vector indicating the samples that should be exuded in the expression and FoldChange plots. By default NULL.
exclude.housekeeping.genes	Logic value to indicate whether the housekeeping genes should be excluded in the plot. By default TRUE.
plot.color	Single string to indicate the color to use for the bar plot. Default value: #D1718B.
fix.y.axis	Logic value indicating whether the y-axis of the plots should be kept fixed among all the genes. By default FALSE.
text.size	Numeric value to indicate the size of the text for the number above the bars. Default 3.
x.labels.rotation	Numeric value indicating the degrees of x-axis's labels rotation. By default 45.

Value

The function returns a list containing:

• mean.reps.data.table: a list of data.frames, one per housekeeping gene and the mean of all housekeeping genes, containing the number of reps (n), SD and SEM for each sample-target combination for both normalized expression and FoldChanges;

• mean.reps.exp.plots: a list of a plots, one per housekeeping gene, showing the replicates' normalized expression over the reference Sample (facet_wrapped by gene);

• mean.reps.FC.plots: a list of a plots, one per housekeeping gene and the mean of all housekeeping genes, showing the replicates' mean FoldChange expression over the reference Sample (facet_wrapped by gene).

sebastian-gregoricchio/Rseb documentation built on Sept. 4, 2024, 1:59 p.m.